In a “humble petition” to the “honourable” members of the Commons, the Church concludes: “Your petitioners therefore humbly pray your Honourable House that the Bill may not be allowed to pass into law as it now stands.”

Sir Tony Baldry, the Tory MP and Second Church Estate’s Commissioner, said: “I would hope HS2 will be willing to engage and consider what they can do to mitigate the impact on churchyards and remains they may have to inter.

“It is a serious point. It’s a matter of common decency that when people are buried in consecrated ground they expect their remains not to be disturbed except in truly exceptional circumstances.”

Other high-profile petitioners have also lobbied parliament to stop the controversial scheme in its current form.

They include Earl Spencer, brother of the late Diana, Princess of Wales, and Lord Rothschild, who both own land along the route. Other “blue blood” objectors include Nicholas and Alice van Cutsem, close friends of the Duke of Cambridge, and Lord Richard Wellesley, a descendant of the Duke of Wellington.

They have complained that the link will cut through their estates, cause “intolerable” noise and damage areas of outstanding natural beauty.

According to a parliamentary submission by the Archbishop’s Council, the HS2 line will pass through three consecrated burial grounds.

The expansion of Euston station in north London will require more than 30,000 graves to be exhumed at St James’ Gardens, an 18th century burial ground.

Among those buried there are James Christie, the founder of the auction house, Charles Fitzroy, the First Baron Southampton, and the painters George Morland and John Hoppner.

The remains of 2,600 people will have to be exhumed from a 12th century graveyard in Stoke Mandeville, Bucks to make way for the line, along with remains beneath Park Street in Birmingham where a new terminal is being built.

The Church of England is keen to avoid a repeat of the excavation of St Pancras station during the building of the Channel Tunnel rail link, when graves were dug up with JCBs.

The petition states: “[The clauses in the legislation] do not make adequate provision to ensure that during and after the removal of human remains they are treated in a decent and reverent manner or that they are subsequently reinterred in consecrated land.

The council compares the High Speed Rail Bill to other legislation which affords greater protection to the dead.

Under the Town and Country Planning Act, bishops have the right to put in place regulations directing the “manner of removal” and “reinterment of any human remains and monuments”.

The council warns that the High Speed Rail Bill has failed to strike the “proportionate balance” between the right of the Church to consecrate burial grounds and the “general needs of the community”.

The Church is also concerned about a number of churches along the route, including Chetwode St Peter’s in Buckinghamshire.

A Church of England source said: “We are concerned it [the church] will have to close, it splits the settlement in two and people are likely to move out. The line is just 200 metres from the church and there will be significant noise and vibration. It will shatter the rural idyll.”

It is backing a petition from the church which warns that the high speed railway line will disrupt services, greatly reduce the congregation as parishioners move to other areas and could force it to close.

A Church of England spokesman said: “In terms of 'opposition’ the Church of England is not opposing HS2 per se, rather we are petitioning for a technical change to the Bill.”

The spokesman said that the Church wanted the Government to introduce a clause to offer greater protections to graveyards.

A Department for Transport spokesman said: “Throughout the development of HS2, burial grounds have been avoided as far as practicable. We understand that the removal of human remains to enable HS2 to progress is a sensitive and emotive issue, which is why this issue is specifically dealt with in the Hybrid Bill and why HS2 Ltd recently published a paper setting out how it would deal with affected burial sites along the route.

“Though the affected burial sites at Euston, Stoke Mandeville and Birmingham have not been in use for more than 100 years, HS2 Ltd will ensure that the affected remains are treated with dignity, respect and care.”